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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA

Basic information

species Zea mays
transcript GRMZM2G062210_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 5
----gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
     | |  |||    | || | | |  |  ||| | |    | ||  |   ||||  ||  |||    ||||||||| ||||||||||||||||||||||| ||||| || |||||||||||||| |||||||||||||| || |||||||||||||| |||||||| |||||||
gtactttatcctctattggcgatgc-ctagggattccaggttgtgttaggttttgctcatatgtgat-tttctgcagGCTCGGATAGACTCCCACAACAAGATTCTTTATGCGAGGCATGCTGACCAAAGAAATGCAACTTTTCAACGTGTCCTTCAAACAGGCAATGAGTTTGAGA

upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ06457 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
||||     |  | | |   ||  |  | |||||    | | |   || || | |               ||||||||||| ||||||||||||||||| || |||||  | || ||||||||  | || ||| | || || || | | | ||||| ||| | |||||  || 
gtaagctagaacaatggtggctgtt--agtttct---tactcttcacgttgttgc---------------cagGCCCGGATCGACTCCCACAACAAGATTCTCTACGCTCGCCACGCTGACCAACGCAAGGCATCGTTTCAACGCGCCATGCAAACAGGCTACGACTTCCAGC

upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ08729 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgc-agGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
                        | |  |   ||     ||| |  | | |||     | |      ||| |||||||||| ||||||||||||||||| || |||||  | || ||||||||  | || ||| | || || || | | | ||||| ||| | |||||  || 
-----------------------gtaagctagatggatggttttttagtttcttactcttcacgttgttgccagGCCCGGATCGACTCCCACAACAAGATTCTCTACGCTCGCCACGCTGACCAACGCAAGGCATCGTTTCAACGCGCCATGCAAACAGGCTACGACTTCCAGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60339643|gb|DN206616.1|DN206616
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|211125416|gb|FL031454.1|FL031454
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|22819870|gb|BU499960.1|BU499960
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|211097205|gb|FL379410.1|FL379410
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|60345822|gb|DN212795.1|DN212795
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|60357208|gb|DN224181.1|DN224181
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|20811311|gb|BQ295789.1|BQ295789
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
EST: gi|211125417|gb|FL031455.1|FL031455
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TATATCTGTTGACCTCAACACGATGGCAGCCGCCTTTAAGACTTCGGTCTCCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

TATATCTGTTGACCTCAACACGATGGCAGCCGCCTTTAAGACTTCGGTCTCCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

TATATCTGTTGACCTCAACACGATGGCAGCCGCCTTTAAGACTTCGGTCTCCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

TATATCTGTTGACCTCAACACGATGGCAGCCGCCTTTAAGACTTCGGTCTCCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
                                  ttctaac  putative branch site (score: 79)
                                              cctctgc  putative PPT
      tgaaattt  TA-rich tract